South Africa arrive at the Principality Stadium having already lost seven of 11 Tests in 2016, equalling their record for the most defeats in a season since returning to international rugby in 1992 from apartheid-induced isolation.
They hit a new low last week as they suffered a maiden loss to Italy, going down 20-18 in Florence.
Habana returned from injury to score the opening try against Italy, taking his tally to 67 tries -- just two shy of the all-time Test record -- in 124 appearances.
Yet the 33-year-old Habana has been dropped for the first time when fit and available during an illustrious, 124-cap career.
What's more, the 2007 World Cup-winner, who now plays his club rugby for French giants Toulon, isn't even on the bench.
Habana's place against Wales is taken by debutant Jamba Ulengo. Fellow new cap Rohan Janse van Rensburg replaces Damian de Allende in midfield with Uzair Cassiem, the third debutant in the XV, taking over from injured loose forward Willem Alberts.
A revamped backline sees the return of Faf de Klerk (scrum-half) and Elton Jantjies (fly-half) while Johan Goosen starts at fullback in place of Willie le Roux.
"I would not go as far as saying it is the end for him," said Coetzee of Habana.
"He has not just got a role to play on the field, but a massive role off it for South African rugby.
"What he has been doing this week is mentor Jamba Ulengo and share his knowledge and experience.
If nothing else, Coetzee's selection heaped the pressure on Wales -- themselves castigated after last week's lacklustre 33-30 home win over Japan -- to record just a third victory in 32 Tests against the Springboks.
By dropping Habana, under-fire Coetzee has provided more potential ammunition for his critics, but he said his selection was made with one eye on the 2019 World Cup in Japan.
"Our selection is also keeping in mind of the process and necessity to build towards 2019," said Coetzee, who may not get the chance to see out the four-year contract he signed last year if the Springboks lose on Saturday.
"The toughest part is dealing with the emotions of people, players and the management team," said Coetzee. "We know South Africans are hurting back home.
"Rugby is rock bottom at the moment, and there can only be one way -- up," he added, ahead of South Africa's final Test of 2016.
"I am really positive about the future. I back this young team fully, and I will be really pleased if they give their all and leave nothing out there.
Wales captain Sam Warburton has been ruled out with a 'stinger' injury, with his back-row place in a team now led by prop Gethin Jenkins taken by Dan Lydiate.
Several players who missed the Japan game have been recalled, including wing George North, fly-half Dan Biggar and lock Luke Charteris.
"We want to play, but there has to be a sensibility about when," said Wales coach Rob Howley, in charge while Warren Gatland is seconded to the British and Irish Lions. "We have always encouraged our squad to play because we feel we have X-factor players.
"Against Japan, we hurt ourselves," the former Wales and Lions scrum-half added. "The three tries Japan scored came from us having had the ball.
"We won the game, but the performance and the expectation of the players and coaches came up short."